Genetic mosaics, in which somatic cells of different genotypes reside in the same animal, have been widely used to study biological processes in multicellular organisms. By knocking out a candidate gene of interest in a defined population of cells at a desirable time, one can study gene function in biological processes of interest while bypassing possible requirements for the gene in other tissues or at earlier developmental stages. One can also analyze the cell autonomy of gene function if the candidate gene is removed only in small populations of defined cell types. In addition, mosaic analysis can be used to create animal models for human diseases that result from somatic mutations. We have recently developed a genetic mosaic system in mice termed MADM (for Mosaic Analysis with Double Markers), which allows simultaneous in vivo labeling and genetic manipulation of defined neuronal populations, down to the level of single isolated neurons. We have established MADM at the ROSA26 locus of mouse chromosome 6 to show that 1) inter-chromosomal recombination can occur efficiently the Cre-loxP system; 2) MADM can be used to create conditional knockouts in small populations of labeled cells to study gene function; 3) MADM can be used to investigate the relationship between neuronal lineage and wiring patterns. We have also preliminary data that MADM can be expanded to other chromosomes using targeted knockin and random ES cell transgenesis approaches. We now propose to expand the MADM system to all mouse chromosomes so that one can perform MADM-based mosaic analysis for vast majority of genes in the mouse. We also propose to use the features afforded by MADM to investigate the role of neuronal activity in morphological maturation of individual neurons and in circuit development. Lastly, we will apply MADM to study several genes implicated in human neurological diseases, including lissencephaly and autism- spectrum disorders.